Peter N. Robinson

A Phenotypic Paradigm for Cerebral Palsy Genetics

The paper identifies pathogenic variants in 15.8% of CP patients and finds only 16 of 60 genes have significant CP association.

Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis

Ontologizer 3 provides a desktop tool for GO enrichment analysis using frequentist and Bayesian methods, showing higher precision with the Bayesian approach on simulated data.

Data-driven prioritization of mouse strains for improved preclinical modeling of rare and common disease

This paper introduces a genomic framework to prioritize mouse strains for preclinical disease modeling, showing high sensitivity in predicting strain vulnerability to diseases.

Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools

This study benchmarks large language models against a traditional diagnostic tool for genetic disease diagnosis using 5,213 case reports, finding LLMs lag behind in accuracy.

GA4GH Phenopacket-Driven Characterization of Genotype-Phenotype Correlations in Mendelian Disorders

The paper introduces GPSEA, a tool using GA4GH Phenopackets to analyze genotype-phenotype correlations in Mendelian disorders, identifying 225 significant associations across 85 cohorts.

Performance of Information Theory Derived Semantic Similarity Algorithms for Differential Diagnosis and Clustering

The paper compares semantic similarity algorithms for differential diagnosis and clustering using HPO, finding Phenomizer performs best for ranking and non-normalized algorithms for clustering.

Development of self-phenotyping tools to empower patients and improve diagnostics

The paper evaluates two self-phenotyping tools, showing that GenomeConnect provides more accurate phenotype profiles while Phenotypr offers greater precision and user preference for its autocomplete format.

Long-read single-cell RNA sequencing uncovers cell-type specific transcript regulation in COVID-19

This study uses long-read single-cell RNA sequencing to identify cell-type specific alternative splicing changes in COVID-19 patients compared to healthy controls.

Linking international registries to FHIR and Phenopackets with RareLink: a scalable REDCap-based framework for rare disease data interoperability

RareLink enables interoperability between REDCap and global health standards by exporting data to Phenopackets and FHIR, improving rare disease research scalability and data reuse.

Replacing non-biomedical concepts improves embedding of biomedical concepts

The paper replaces non-biomedical synonyms with biomedical terms to improve concept embeddings using Word2Vec, reducing mean intracluster distance by 8%.

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

PhEval provides a standardized framework to benchmark phenotype-driven variant and gene prioritisation algorithms using real-world patient data and controlled test corpora.

The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics

The paper introduces uPheno, a framework for cross-species phenomics integration by harmonizing phenotype data across species and ontologies.

A de novo variant in PAK2 detected in an individual with Knobloch type 2 syndrome

The paper identifies a novel de novo PAK2 variant in a patient with Knobloch syndrome type 2, supporting PAK2's role in the disorder and expanding its clinical features.

Intrinsic-Dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing

This paper introduces a method to guide dimensionality reduction and data fusion in multi-omics data by analyzing intrinsic dimensionality, showing improved performance in predicting survival outcomes.

Alternative splicing is coupled to gene expression in a subset of variably expressed genes

The paper shows that alternative splicing is coupled to gene expression in a subset of variably expressed genes across multiple tissues.

A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery

The paper presents a large-scale corpus of standardized phenopackets for genomic diagnostics and discovery, curated from literature and useful for software testing and genotype-phenotype analysis.

Leveraging Generative AI to Accelerate Biocuration of Medical Actions for Rare Disease

AutoMAxO uses LLMs to semi-automate MAxO curation for rare diseases, identifying 538 confirmed disease-treatment annotations from 4,918 medical abstracts.

Fine-tuning of conditional Transformers for the generation of functionally characterized enzymes

This paper introduces Finenzyme, a Protein Language Model that improves EC category prediction through fine-tuning, generating functionally similar enzymes with preserved structure and function.

Lethal phenotypes in Mendelian disorders

This paper curates human essential genes based on lethality in Mendelian disorders and explores their relationships with constraint metrics and viability data.

Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine

The paper uses ontologies to integrate clinical, pathological, and molecular kidney data for precision medicine analysis.

Phenomics Assistant: An Interface for LLM-based Biomedical Knowledge Graph Exploration

Phenomics Assistant is a chat-based interface that uses LLMs to query the Monarch knowledge graph, improving reliability for non-expert users to explore disease-gene-phenotype relationships.

Rare disease gene association discovery from burden analysis of the 100,000 Genomes Project data

The paper identifies 88 novel rare disease-gene associations using a burden analysis framework on whole genome sequencing data from the 100,000 Genomes Project, with potential clinical impact for undiagnosed cases.

Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms

This paper standardizes terminology for describing disease-gene relationships to improve variant classification and genetic test interpretation.

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

This paper introduces OBA, a formalized ontology for biological attributes to facilitate data integration across phenotypic, genetic, and environmental data.

Computing Minimal Boolean Models of Gene Regulatory Networks

The paper develops an algorithm to compute minimal Boolean models of gene regulatory networks from single-cell RNA-Seq data, demonstrating its effectiveness on a public dataset.

Node-degree aware edge sampling mitigates inflated classification performance in biomedical graph representation learning

The paper introduces a degree-aware edge sampling method to reduce performance inflation in biomedical graph representation learning caused by imbalanced edge degree distributions.

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

The paper introduces the GA4GH Phenopacket schema to standardize the exchange of phenotypic data for precision medicine applications.

An algorithmic framework for isoform-specific functional analysis

The paper introduces isopret, an algorithm for predicting isoform-specific functions using RNA-seq data, and shows that expression and splicing regulate distinct biological functions.

Betacoronavirus-specific alternate splicing

The paper investigates differential alternative splicing in cells infected by betacoronaviruses and finds characteristic patterns linked to viral load and gene function.

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

The paper introduces the GA4GH Variation Representation Specification (VRS), a framework for precise and federated representation of molecular variation, with a reference implementation and community resources available online.